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BioMart Central Portal: an open database network for the biological community

Jonathan M Guberman et al. Database (Oxford). .

Abstract

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

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Figures

Figure 1.
Figure 1.
Databases available on the BioMart Central Portal and their host countries (April 2011).
Figure 2.
Figure 2.
Each individual server hosts its own instance of BioMart retrieving data from its own local database backend. Central Portal offers a unified access point to all of these databases, distributing queries to the appropriate servers.
Figure 3.
Figure 3.
The BioMart Central Portal home page. Three main entry points are available: (A) Identifier search, (B) Tools and (C) Database search.
Figure 4.
Figure 4.
The Gene Report page for EGFR, displaying data federated from several sources.
Figure 5.
Figure 5.
The sequence retrieval plug-in page.
See this image and copyright information in PMC

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